On Wednesday MPs will vote on a bill which would allow the creation of human/animal hybrid embryos to be used for stem cell research, change the conditions for granting IVF, and possibly liberalise the abortion laws.

The passage through Parliament of the Human Fertilisation and Embryology Bill has been dogged by controversy. Failed attempts to outlaw late abortion have dominated the debate, while scientists, medical ethics experts and religious leaders have clashed over the hybrid embryo issue.

Defenders of the bill have repeatedly stressed the importance of gaining consent from anyone whose tissue is taken for the creation of human/animal hybrid embryos.

It can now be revealed that a Government amendment, agreed after the main parliamentary debates, would allow tissue to be used from people who lack the "mental capacity" to give consent, children whose parents give permission, and anyone who has previously donated samples to hospitals for medical research but can no longer be traced.

Medical ethics experts and religious leaders are furious that the provisions, which they say ride roughshod over basic human rights, have already been agreed by an all-party committee of 17 MPs charged with scrutinising the bill, without any public debate or discussion in the main chambers of Parliament.

Prof David Jones, director of the Centre for Bioethics and Emerging Technologies at St Mary's University College, London, said: "In May we had a public debate about whether or not it is a good thing to create hybrid embryos.

"Now it transpires that just weeks later, with no public debate at all, the Government inserted these amendments which cross a fundamental line in medical ethics by presuming consent in many cases. I think it is totally objectionable, and I really worry that this will create a backlash against medical research."

He said he feared that someone who had strong ethical concerns about the creation of embryos could have their original wishes overruled, if they developed a disease such as Alzheimers and decisions about consent were taken by someone who did not know them.

Prof John Haldane, director of the Centre for Philosophy and Public Affairs at the University of St Andrews, described the draft legislation as a "mess" which would sweep away 25 years of progress in medical ethics.

"The most intimate thing over which you have control is your body and its fate; and this is total violation of that basic right," he said.

Under the amendment, if a person was deemed unable to give consent their carer would make a decision on their behalf. If the person did not have a carer, researchers would nominate a person to make the judgement. If scientists wanted to use human tissues already donated for research, perhaps during a medical procedure, but were unable to trace the donors because the research had been anonymised or the person had moved house, the samples could also be used.

Labour MP Dr Ian Gibson, one of the members of the committee which passed the amendments proposed by public health minister Dawn Primarolo, said he feared that major changes were being made with little consideration by Parliament and almost no public debate.

"I am really worried that this whole debate has become hijacked by the issue of abortion, and that really significant issues like this have not had a good airing, and are unlikely to do so this week when the bill gets to its final stage, despite the fact this is a once-in-a-lifetime chance to make some fundamental decisions," he said.

Dr Gibson said he personally opposed any use of tissue without consent. "There has to be consent, there can be no substitution for it. If you are not sure it is what the person would have wanted, that is just not good enough," he said.

Jim McManus, from the Catholic Bishops Conference of England and Wales, described the changes to the bill as a "macabre" prospect. He said: "This is a reckless step backwards, and it rides roughshod over a basic human right."

Scientists say combining animal embryos with human cells would allow an expansion in research, which is currently limited by numbers of donations of human embryos.

Catherine Elliot, from the Medical Research Council, said such research could provide a "powerful tool" to examine the development and treatment of different diseases. She said research would "rarely" be carried out without consent, because under the amendment, ethics committees must be satisfied the same research could not have been carried out using tissue from patients who had granted permission.

Charities representing people with degenerative diseases and learning disabilities last night said they knew little about the changes to the bill, which have received almost no publicity.

Mencap and The Motor Neurone Disease Association said they would now be studying the amendment, while the Alzheimer's Society expressed some reservations, but said it was optimistic that ethics committees would take cautious decisions about the use of tissue if consent had not been obtained.

A counter-amendment, deleting the changes to consent, has been listed for the bill's final debate on Wednesday, but campaigners fear it is unlikely to be discussed, as it is one of dozens vying to be chosen for the bill's final debate before MPs vote.

The Department of Health said the amendment came in response to concerns raised in the House of Lords about the use of cells from children who were not able to give consent, and adults who lacked mental capacity to consent to research into serious illnesses from which they suffered.

A spokesman said ministers were satisfied that a case had been made which justified limited exceptions from the European Convention on Human Rights.

Although MPs have been given a free vote on some aspects of the bill, including the clauses governing the creation of hybrid embryos, Labour MPs will be under a three-line whip to support the changes on consent, which are dealt with in a separate part of the legislation.